NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
Q5RCE4 UniProt NPD GO	THAP1_PONPY	THAP domain-containing protein 1	0.67	+	nuc	0	Nucleus; nucleoplasm (By similarity). And PML nuclear bodies (By similarity)				213
Q96KP6 UniProt NPD GO	TNIP3_HUMAN	TNFAIP3-interacting protein 3 (Listeria-induced gene protein) (A20-binding inhibitor of NF-kappa-B a ...	0.67	-	nuc	0			608019		319
Q9NYB0 UniProt NPD GO	TE2IP_HUMAN	Telomeric repeat-binding factor 2-interacting protein 1 (TRF2-interacting telomeric protein Rap1) (h ...	0.67	-	nuc	0	Nucleus. Colocalizes with telomeric DNA in interphase and metaphase cells	nuclear chromosome [TAS]	605061	1FEX	399
Q91Z38 UniProt NPD GO	TTC1_MOUSE	Tetratricopeptide repeat protein 1 (TPR repeat protein 1)	0.67	-	nuc	0					292
Q9UDY2 UniProt NPD GO	ZO2_HUMAN	Tight junction protein ZO-2 (Zonula occludens 2 protein) (Zona occludens 2 protein) (Tight junction ...	0.67	+	nuc	0	Peripheral membrane. Cytoplasmic side. Also nuclear under environmental stress conditions and in mig ...		607748		1190
Q9BXR5 UniProt NPD GO	TLR10_HUMAN	Toll-like receptor 10 precursor	0.67	-	mit	1	Membrane; single-pass type I membrane protein (By similarity)	membrane [TAS]	606270		811
Q9QUN7 UniProt NPD GO	TLR2_MOUSE	Toll-like receptor 2 precursor (CD282 antigen)	0.67	-	end	1	Cell membrane; single-pass type I membrane protein. Phagosome; phagosomal membrane; single-pass type ...	plasma membrane [IDA]			784
Q9FEC4 UniProt NPD GO	RAA3_CHLRE	Trans-splicing factor Raa3, chloroplast precursor	0.67	-	nuc	0	Plastid; chloroplast; chloroplast stroma				1783
Q5R405 UniProt NPD GO	SPT5H_PONPY	Transcription elongation factor SPT5 (DRB sensitivity-inducing factor large subunit) (DSIF large sub ...	0.67	-	nuc	0	Nucleus (By similarity)				1083
O22059 UniProt NPD GO	CPC_ARATH	Transcription factor CAPRICE	0.67	-	nuc	0	Nucleus	nucleus [IDA]			94
P43694 UniProt NPD GO	GATA4_HUMAN	Transcription factor GATA-4 (GATA-binding factor 4)	0.67	-	nuc	0	Nucleus	nucleus [NAS]	607941		442
P23922 UniProt NPD GO	HBP1A_WHEAT	Transcription factor HBP-1a (Histone-specific transcription factor HBP1)	0.67	+	nuc	0	Nucleus				349
Q14469 UniProt NPD GO	HES1_HUMAN	Transcription factor HES-1 (Hairy and enhancer of split 1) (Hairy-like) (HHL) (Hairy homolog)	0.67	-	nuc	0	Nucleus		139605		280
Q9UTL5 UniProt NPD GO	TF3A_SCHPO	Transcription factor IIIA (Factor A) (TFIIIA)	0.67	-	nuc	0	Nucleus (By similarity)				374
Q24318 UniProt NPD GO	TDP_DROME	Transcription factor dp	0.67	+	nuc	0	Nucleus (Potential)	Myb complex [IDA] Rb-E2F complex [IDA]			445
Q93705 UniProt NPD GO	UNC3_CAEEL	Transcription factor unc-3 (Uncoordinated protein 3) (CEO/E)	0.67	-	nuc	0	Nucleus (Potential)				491
Q05021 UniProt NPD GO	TAF7_YEAST	Transcription initiation factor TFIID subunit 7 (TBP-associated factor 7) (TBP-associated factor 67 ...	0.67	+	nuc	0	Nucleus	nucleus [IDA] transcription factor TFIID complex [IDA]			590
P28347 UniProt NPD GO	TEAD1_HUMAN	Transcriptional enhancer factor TEF-1 (TEA domain family member 1) (TEAD-1) (Protein GT-IIC) (Transc ...	0.67	-	nuc	0	Nucleus		189967		426
O19011 UniProt NPD GO	TGFB1_HORSE	Transforming growth factor beta-1 precursor (TGF-beta-1) [Contains: Latency-associated peptide (LAP) ...	0.67	-	exc	0	Secreted protein				390
P07200 UniProt NPD GO	TGFB1_PIG	Transforming growth factor beta-1 precursor (TGF-beta-1) [Contains: Latency-associated peptide (LAP) ...	0.67	-	exc	0	Secreted protein	extracellular matrix (sensu Metazoa) [ISS] extracellular space [ISS]			390
Q8NET8 UniProt NPD GO	TRPV3_HUMAN	Transient receptor potential cation channel subfamily V member 3 (TrpV3) (Vanilloid receptor-like 3) ...	0.67	+	end	6	Membrane; multi-pass membrane protein		607066		790
Q8C006 UniProt NPD GO	TRI35_MOUSE	Tripartite motif-containing protein 35 (Macrophage-derived apoptosis-inducing RBCC protein) (Protein ...	0.67	-	cyt	0	Cytoplasm. Nucleus. Found predominantly in cytoplasm with a granular distribution. Found in punctuat ...	cytoplasm [IDA] nucleus [IDA]			501
Q61333 UniProt NPD GO	TNAP2_MOUSE	Tumor necrosis factor, alpha-induced protein 2 (Primary response gene B94 protein)	0.67	-	cyt	0					650
Q9P4U6 UniProt NPD GO	TCSB_EMENI	Two-component system protein B precursor (EC 2.7.13.3) (Protein NHK1) (SLN1 homolog)	0.67	-	exc	2 *	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [NAS]			1070
Q24145 UniProt NPD GO	SHARK_DROME	Tyrosine-protein kinase shark (EC 2.7.10.2)	0.67	-	nuc	0	Cytoplasm. Apical expression in cephalic furrow and tracheal cells. Limited to luminal surface and a ...	cytoplasm [IDA]			939
P45429 UniProt NPD GO	SNRPA_XENLA	U1 small nuclear ribonucleoprotein A (U1 snRNP protein A) (U1A protein) (U1-A)	0.67	-	nuc	0	Nucleus				282
Q06679 UniProt NPD GO	UTP4_YEAST	U3 small nucleolar RNA-associated protein 4 (U3 snoRNA-associated protein 4)	0.67	+	nuc	0	Nucleus; nucleolus	small nucleolar ribonucleoprotein complex [IPI]			776
P20053 UniProt NPD GO	PRP4_YEAST	U4/U6 small nuclear ribonucleoprotein PRP4	0.67	-	cyt	0	Nucleus (Probable)	U4/U6 x U5 tri-snRNP complex [IDA]			465
O94245 UniProt NPD GO	YJ14_SCHPO	UPF0300 protein C737.04 in chromosome III	0.67	-	cyt	0	Cytoplasm				421
Q6GL38 UniProt NPD GO	UBTD1_XENTR	Ubiquitin domain-containing protein 1	0.67	-	nuc	0					240
Q9NPD8 UniProt NPD GO	UBE2T_HUMAN	Ubiquitin-conjugating enzyme E2 T (EC 6.3.2.19) (Ubiquitin-protein ligase T) (Ubiquitin carrier prot ...	0.67	-	nuc	0				1YH2	197
Q7ZY08 UniProt NPD GO	UBE2T_XENLA	Ubiquitin-conjugating enzyme E2 T (EC 6.3.2.19) (Ubiquitin-protein ligase T) (Ubiquitin carrier prot ...	0.67	-	nuc	0					192
Q6CWM4 UniProt NPD GO	BRE1_KLULA	Ubiquitin-protein ligase BRE1 (EC 6.3.2.-)	0.67	-	nuc	0	Nucleus (By similarity)				663
Q86UX7 UniProt NPD GO	URP2_HUMAN	Unc-112-related protein 2 (Kindlin-3) (MIG2-like)	0.67	-	cyt	0	Cytoplasm (Probable). Membrane-associated in chronic lymphocytic leukemia (CLL) cells		607901		667
P34281 UniProt NPD GO	YKK4_CAEEL	Uncharacterized protein C02F5.4	0.67	-	nuc	0					315
Q8BU04 UniProt NPD GO	CN130_MOUSE	Uncharacterized protein C14orf130 homolog	0.67	+	nuc	0					425
P39723 UniProt NPD GO	YAE7_YEAST	Uncharacterized protein YAL047C	0.67	-	nuc	0		outer plaque of spindle pole body [IDA]			622
P53203 UniProt NPD GO	YG14_YEAST	Uncharacterized protein YGR004W	0.67	-	end	4	Membrane; multi-pass membrane protein (Potential)	integral to peroxisomal membrane [IDA]			462
P38783 UniProt NPD GO	YHL9_YEAST	Uncharacterized protein YHR059W	0.67	-	mit	0		mitochondrion [IDA]			130
P40465 UniProt NPD GO	YIN2_YEAST	Uncharacterized protein YIL132C	0.67	+	nuc	0		cytoplasm [IDA] nucleus [IDA]			213
Q07956 UniProt NPD GO	USF_STRPU	Upstream stimulatory factor (USF) (SPF1)	0.67	+	nuc	0	Nucleus				265
P22415 UniProt NPD GO	USF1_HUMAN	Upstream stimulatory factor 1 (Major late transcription factor 1)	0.67	+	nuc	0	Nucleus	nucleus [TAS]	191523	1AN4	310
O02818 UniProt NPD GO	USF1_RABIT	Upstream stimulatory factor 1 (Major late transcription factor 1)	0.67	+	nuc	0	Nucleus				310
Q9NWZ5 UniProt NPD GO	UCKL1_HUMAN	Uridine/cytidine kinase-like 1	0.67	-	cyt	0					548
Q6CM12 UniProt NPD GO	BRO1_KLULA	Vacuolar protein-sorting protein BRO1 (BRO domain-containing protein 1)	0.67	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity)				813
Q3HXX5 UniProt NPD GO	NGFV4_TROCA	Venom nerve growth factor 4 precursor (vNGF-4)	0.67	-	exc	0	Secreted protein				244
Q9UIW0 UniProt NPD GO	VAX2_HUMAN	Ventral anterior homeobox 2	0.67	+	nuc	0	Nucleus (Probable)		604295		290
Q9PU20 UniProt NPD GO	VAX2A_XENLA	Ventral anterior homeobox 2a (Xvax2)	0.67	+	nuc	0	Nucleus (By similarity)				302
Q90953 UniProt NPD GO	CSPG2_CHICK	Versican core protein precursor (Large fibroblast proteoglycan) (Chondroitin sulfate proteoglycan co ...	0.67	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				3562
Q9MZL7 UniProt NPD GO	CACB1_BOVIN	Voltage-dependent L-type calcium channel subunit beta-1 (CAB1) (Calcium channel voltage-dependent su ...	0.67	-	nuc	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein; cytoplasmic side				598

You are viewing entries 15551 to 15600 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.